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Code Examples
=============

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Plotting examples
-----------------

This is a gallery containing some plotting examples.





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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows you how to generate riverplots to compare categorical columns, for example t...">

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  .. image:: /auto_examples/plotting/images/thumb/sphx_glr_plot_riverplot_thumb.png
    :alt: Comparing categorical variable

  :ref:`sphx_glr_auto_examples_plotting_plot_riverplot.py`

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      <div class="sphx-glr-thumbnail-title">Comparing categorical variable</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows you some of the different plots you can use to plot gene expression.">

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  .. image:: /auto_examples/plotting/images/thumb/sphx_glr_plot_split_gene_expression_thumb.png
    :alt: plotting gene expression

  :ref:`sphx_glr_auto_examples_plotting_plot_split_gene_expression.py`

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      <div class="sphx-glr-thumbnail-title">plotting gene expression</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows you the inbuilt quality control plots from besca.">

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  .. image:: /auto_examples/plotting/images/thumb/sphx_glr_plot_qc_thumb.png
    :alt: quality control plots

  :ref:`sphx_glr_auto_examples_plotting_plot_qc.py`

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      <div class="sphx-glr-thumbnail-title">quality control plots</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to generate celltype quantification plots. These types of plots  ...">

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  .. image:: /auto_examples/plotting/images/thumb/sphx_glr_plot_celltype_quantification_thumb.png
    :alt: Visualize cell fractions

  :ref:`sphx_glr_auto_examples_plotting_plot_celltype_quantification.py`

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      <div class="sphx-glr-thumbnail-title">Visualize cell fractions</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows you how to generate plots to visualize the chosen filter threshold. This way...">

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  .. image:: /auto_examples/plotting/images/thumb/sphx_glr_plot_filtering_thumb.png
    :alt: filtering functions

  :ref:`sphx_glr_auto_examples_plotting_plot_filtering.py`

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      <div class="sphx-glr-thumbnail-title">filtering functions</div>
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Preprocessing
-------------

This section highlights some of the features of the preprocessing functions included within BESCA.


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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates the entire process of filtering out cells/genes ob subpar quality bef...">

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  .. image:: /auto_examples/preprocessing/images/thumb/sphx_glr_plot_example_filtering_thumb.png
    :alt: performing filtering using besca

  :ref:`sphx_glr_auto_examples_preprocessing_plot_example_filtering.py`

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      <div class="sphx-glr-thumbnail-title">performing filtering using besca</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to perform highly variable gene selection, PCA, nearest neighbor ...">

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  .. image:: /auto_examples/preprocessing/images/thumb/sphx_glr_plot_pca_neighbors_clustering_thumb.png
    :alt: cluster generation

  :ref:`sphx_glr_auto_examples_preprocessing_plot_pca_neighbors_clustering.py`

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      <div class="sphx-glr-thumbnail-title">cluster generation</div>
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Tools
-----

This section contains all examples related to besca tools.


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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates who to perform a reclustering on a selected subset of leiden clusters...">

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  .. image:: /auto_examples/tools/images/thumb/sphx_glr_plot_reclustering_function_thumb.png
    :alt: reclustering on specific leiden clusters

  :ref:`sphx_glr_auto_examples_tools_plot_reclustering_function.py`

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      <div class="sphx-glr-thumbnail-title">reclustering on specific leiden clusters</div>
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Workflows
---------

Demonstration workflows showing you how to peform certain tasks


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    <div class="sphx-glr-thumbcontainer" tooltip="An example workflow using the PBMC3k dataset included with besca illustrating how to annotate c...">

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  .. image:: /auto_examples/workflows/images/thumb/sphx_glr_plot_celltype_annotation_thumb.png
    :alt: Annotate celltypes

  :ref:`sphx_glr_auto_examples_workflows_plot_celltype_annotation.py`

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      <div class="sphx-glr-thumbnail-title">Annotate celltypes</div>
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.. toctree::
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   /auto_examples/plotting/index.rst
   /auto_examples/preprocessing/index.rst
   /auto_examples/tools/index.rst
   /auto_examples/workflows/index.rst



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    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_